TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv1678/-:

update plot	correlation	link to info on gene
Rv0940c/-	(cc=0.5598)	info on Rv0940c/-
Rv2738c/-	(cc=0.5484)	info on Rv2738c/-
Rv2544/lppB	(cc=0.4987)	info on Rv2544/lppB
Rv2558/-	(cc=0.472)	info on Rv2558/-
Rv3473c/bpoA	(cc=0.4718)	info on Rv3473c/bpoA
Rv1167c/-	(cc=0.4715)	info on Rv1167c/-
Rv1903/-	(cc=0.4691)	info on Rv1903/-
Rv3045/adhC	(cc=0.468)	info on Rv3045/adhC
Rv3397c/phyA	(cc=0.4679)	info on Rv3397c/phyA
Rv0042c/-	(cc=0.465)	info on Rv0042c/-

Correlation of Rv1678/- with Rv2738c/-

Normalized LFCs for Rv1678/-:
(description and provenance of datasets)

	Rv1678/-	Rv2738c/-
Fe_supp_jason_reseq	-0.603	-0.415
low_pH_jason_reseq	2.096	1.104
NO_jason_reseq	-0.105	-1.013
B6_jason_reseq	-2.073	-1.973
MHCII_jason_reseq	0.526	-1.598
Isoniazid02	-2.721	-4.829
Rifampicin4	1.032	0.904
Ethambutol3	-2.157	-3.412
Meropenem3	-1.042	-3.54
Vancomycin16	-0.801	-1.417
Rv2680_day32	0.068	-1.982
H37Rv_KO_MarP	-0.673	0.579
hypoxia_3wks	-0.961	-1.388
hypoxia_6wks	0.497	-0.704
glycerol	1.333	1.011
cholesterol	0.264	0.041
AJ	-0.585	-0.632
Bibs02	1.974	0.366
Bibs02c	-0.399	0.826
BL6	0.859	-1.448
BL6a	1.69	0.647
BXD01	0.291	-0.064
BXD010	0.912	0.445
BXD011	1.015	-0.063
BXD03	2.0	0.92
BXD04	1.013	0.058
BXD05	1.302	0.955
BXD06	0.543	0.235
BXD07	1.34	0.432
BXD08	0.878	0.851
BXD09	1.303	0.013
CAST	0.514	-1.875
CCcont	1.385	-1.564
DS01	1.465	-0.89
DS02	0.654	0.274
DS04	1.546	1.116
DS0c	-0.11	-1.353
GP01	-0.077	-0.109
GP02	-1.089	-0.894
GP0c	0.573	0.107
NOD	0.264	0.571
NZO	0.279	-0.139
PWK	-0.205	-0.997
H37Rv_KO_CtpC	1.028	1.283
H37Rv_KO_CtpD	2.483	0.387
H37Rv_KO_Rv1272	0.501	0.226
H37Rv_KO_SugABC	-1.066	-1.147
H37Rv_KO_MbtN	2.197	0.393
Trans05	2.198	1.008
macrophage_unactivated	0.571	-0.657
IL1	1.035	-0.267
Rapamycin	0.436	0.298
Tcell	-0.104	0.456
GMCSF	0.451	-1.048
IFNab	1.206	-0.103
IFNg	-0.235	0.406
IFNg_GMCSF1	-0.496	-0.129
Rv1432_day32	0.0	0.096
Rv1565c_day32	2.098	-0.76
secA2_input	-0.042	0.387
delta_Rv3594	0.858	0.277
delta_Rv3717	1.452	0.147
delta_Rv3811	1.17	0.891
delta_Rv0954	1.47	0.0
PonA1	1.133	0.19
EccD1_KO	0.164	0.576
EspI_KO	0.787	0.063
PE35_KO	0.618	-1.138
PPE68_KO	1.014	-0.243
glycerol2	0.321	-0.958
lignocerate	2.26	-0.401
oleate	-1.983	-1.46
phosphatidylcholine	1.401	-0.287
acetate	2.522	0.048
glucAc	2.538	-0.127
Rv0950ko	-0.935	0.917
Rv1096ko	-0.766	-0.051
Rv3684ko	0.223	0.688
delta_otsA_trehalose	-1.065	0.382